Araştırma Çıktıları
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Item Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection(SPRINGER HEIDELBERG, 2022-01-01) Cirit, Osman Sezer; Mutlu, Esvet; Sancak, Banu; Kocagoz, Tanil; Can, Ozge; Cicek, Candan; Sayiner, Ayca Arzu; Appak, Ozgur; Uyar, Neval Yurttutan; Kulah, Canan; Cicek, Aysegul Copur; Ozgumus, Osman Birol; Altintop, Yasemin Ay; Saatci, Esma; Karsligil, Tekin; Zer, Yasemin; Ozen, Nevgun Sepin; Cekin, Yesim; Karahan, Zeynep Ceren; Evren, Ebru; Karakoc, Ayse Esra; Orhan, Sultan Gulbahce; Mutlu, Derya; Bozdemir, Tugba; Cayci, Yeliz Tanriverdi; Cinar, Canberk; Tasbakan, Meltem; Mert, Merve; Cinar, Ece; Kutsoylu, Oya Ozlem Eren; Kocagoz, Sesin; Erturk, Ayse; Celik, Ilhami; Mete, Ayse Ozlem; Eneyli, Muge Gunalp; Akdemir, Irem; Karakok, Taliha; Inan, Dilara; Atilla, Aynur; Taflan, Sevket Onur; Yoruk, Kagan EtkaMolecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor (TM) Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor (TM) SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9\%) were positive and 98 (22.1\%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor (TM). Antigen Rapid Test Kit was 80.3\% whereas specificity was found to be 87.8\%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7\%, while it increased to 95.7\% in samples 20 <= Ct < 25 and reached 100\% in samples with Ct values below 20. RapidFor (TM) SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.Item Human Metapneumovirus Infection in Adults as the Differential Diagnosis of COVID-19(GALENOS YAYINCILIK, 2021-01-01) Dogan, Lerzan; Akinci, Canan; Sarikaya, Zeynep Tugce; Kaya, Hande Simten Demirel; Zengin, Rehile; Mammadov, Orkhan; Ilksoz, Aylin; Ozdemir, Ilkay Kisa; Eren, Meltem Yonca; Afsar, Nazire; Kocagoz, Sesin; Akinci, Ibrahim OzkanHuman metapneumovirus (HMPV) is a respiratory tract virus identified 18 years prior to severe acute respiratory syndrome coronavirus-2. Both viruses cause acute respiratory failure characterised by a rapid onset of widespread inflammation in the lungs with clinical symptoms similar to those reported for other viral respiratory lung infections. HMPV, more generally known as childhood viral infection, causes mild and self-limiting infections in the majority of adults, but clinical courses can be complicated in risky groups and associated morbidity and mortality are considerable. Moreover, adults are not regularly screened for HMPV and the prevalence of adult HMPV infections in Turkey is unknown, with previous reports in the paediatric population. This should always be kept in mind during the coronavirus disease-2019 pandemic, particularly when neurological complications are added to respiratory findings. In our study, two adult cases of HMPV pneumonia and encephalitis have been recorded.Item Surface-Enhanced Raman Scattering of Bacteria in Microwells Constructed from Silver Nanoparticles(HINDAWI LTD, 2012-01-01) Culha, Mustafa; Yazici, M. Muge; Kahraman, Mehmet; Sahin, Fikrettin; Kocagoz, SesinWhole bacterial cell characterization is critically important for fast bacterial identification. Surface-enhanced Raman scattering (SERS) is proven to be powerful technique to serve such a goal. In this study, the characterization of whole bacterial cells in the microwells constructed from colloidal silver nanoparticles (AgNPs) with ``convective-assembly{''} method is reported. The proper size of the microwells for the model bacteria, Escherichia coli and Staphylococcus cohnii, is determined to be 1.2 mu m from their electron microscopy images. A minimum dilution factor of 20 is necessary for the bacterial samples collected from growth media to diminish the bacterial aggregation to place the bacterial cells into the microwells. The constructed microwell structures are tested for their bacterial SERS performance and compared to the SERS spectra obtained from the samples prepared with a simple mixing of bacteria and AgNPs for the same bacteria. The results indicate that microwell structures not only improve the spectral quality but also increase the reproducibility of the SERS spectra.Item Simple concentration method enables the use of gargle and mouthwash instead of nasopharyngeal swab sampling for the diagnosis of COVID-19 by PCR(SPRINGER, 2021-01-01) Kocagoz, Tanil; Can, Ozge; Yurttutan Uyar, Neval; Aksoy, Ece; Polat, Tuba; Cankaya, Dilara; Karakus, Betul; Mozioglu, Erkan; Kocagoz, SesinSince its emergence in December 2019, SARS-CoV-2 is causing one of the most devastating pandemics in human history. Currently, the most important method for definitive diagnosis of COVID-19 is identification of SARS-CoV-2 RNA in nasopharyngeal swab samples by RT-PCR. Nasopharyngeal swab sampling is a discomforting procedure sometimes with adverse effects, which also poses a risk for infection for the personnel performing the sampling. We have developed a new method for concentrating biological samples, which enabled us to use gargle and mouthwash samples to be used in RT-PCR, for the diagnosis of COVID-19, as an alternative to nasopharyngeal swab samples. We have analyzed nasopharyngeal and gargle and mouthwash samples, before and after concentration, of 363 patients by RT-PCR for the presence of SARS-CoV-2. Among 114 patients in which SARS-CoV-2 was identified in at least one of their samples, the virus was identified in 76 (66.7\%), 67 (58.8\%), and 101 (88.6\%) of nasopharyngeal swab, gargle, and mouthwash samples before and after concentration, respectively. When concentrated by our new method, gargle and mouthwash samples can be used instead of nasopharyngeal samples in identification of SARS-CoV-2 by RT-PCR, with the same or better sensitivity. Eliminating the need for nasopharyngeal sampling will save the patients from an invasive and painful procedure and will lower the risk of infection for the healthcare personnel taking the sample. This easy sampling procedure may decrease the workload of hospitals, shorten the turnaround time of obtaining test results, and thus enable rapid isolation of infected patients.Item Clinical Signs and Diagnostic Tests in Acute Respiratory Infections(SPRINGER INDIA, 2016-01-01) Dut, Raziye; Kocagoz, SesinObjectives To evaluate clinical manifestations of acute respiratory system infectious diseases and specific tests for causative agents in pediatric patients. Methods The authors evaluated children aged 0-16 y with clinical symptoms of acute respiratory tract infections who were administered rapid strep A test and/or throat culture test and/or respiratory viral panel test, from February 2012 through January 2013 at pediatric department of Acibadem Maslak Hospital, Turkey. Results A total of 1654 patients were evaluated